You dont need to complete it, just do the choice. I've changed my alignment from Chaos to Unity just by doing the choice, then skipping the cutscene, going back to town, and then coming back to do it again...

First of all , go to Twilly , the moglin thats in battleon that heals you , say hello , then go to the bottom of the list and press moral compass , and it will show if you are unity , good , chaos , or evil .

You can affact your alinement in many different areas. I think Paxia is a good place to fight different areas that affect your alignment. When wars come up, they will often have choices that give you a chance to change your alignment a bit.